Accuracy of within- and among-family genomic prediction for Fusarium head blight and Septoria tritici blotch in winter wheat.
In this study, two winter wheat populations (DS1 and DS2) consisting of 438 and 585 lines derived from six and eight bi-parental families, respectively, were genotyped with genome-wide single nucleotide polymorphism markers and phenotyped for Fusarium head blight and Septoria tritici blotch severity, plant height and heading date. We used ridge regression-best linear unbiased prediction to investigate the potential of genomic selection under different selection scenarios: prediction across each winter wheat population, within- and among-family prediction in each population, and prediction from DS1 to DS2 and vice versa. Mo...
Source: TAG. Theoretical and Applied Genetics - December 14, 2018 Category: Genetics & Stem Cells Authors: Herter CP, Ebmeyer E, Kollers S, Korzun V, Würschum T, Miedaner T Tags: Theor Appl Genet Source Type: research

Characterisation of barley resistance to rhynchosporium on chromosome 6HS.
a A Abstract KEY MESSAGE: Major resistance gene to rhynchosporium, Rrs18, maps close to the telomere on the short arm of chromosome 6H in barley. Rhynchosporium or barley scald caused by a fungal pathogen Rhynchosporium commune is one of the most destructive and economically important diseases of barley in the world. Testing of Steptoe × Morex and CIho 3515 × Alexis doubled haploid populations has revealed a large effect QTL for resistance to R. commune close to the telomere on the short arm of chromosome 6H, present in both populations. Mapping markers flanking the QTL from both po...
Source: TAG. Theoretical and Applied Genetics - December 13, 2018 Category: Genetics & Stem Cells Authors: Coulter M, Büttner B, Hofmann K, Bayer M, Ramsay L, Schweizer G, Waugh R, Looseley ME, Avrova A Tags: Theor Appl Genet Source Type: research

Breaking the curse of dimensionality to identify causal variants in Breeding 4.
Abstract In the past, plant breeding has undergone three major transformations and is currently transitioning to a new technological phase, Breeding 4. This phase is characterized by the development of methods for biological design of plant varieties, including transformation and gene editing techniques directed toward causal loci. The application of such technologies will require to reliably estimate the effect of loci in plant genomes by avoiding the situation where the number of loci assayed (p) surpasses the number of plant genotypes (n). Here, we discuss approaches to avoid this curse of dimensionality (n&thi...
Source: TAG. Theoretical and Applied Genetics - December 13, 2018 Category: Genetics & Stem Cells Authors: Ramstein GP, Jensen SE, Buckler ES Tags: Theor Appl Genet Source Type: research

Characterization of Pm63, a powdery mildew resistance gene in Iranian landrace PI 628024.
The objective of this study was to characterize a powdery mildew resistance gene in Iranian landrace PI 628024, which exhibited a wide spectrum of resistance to representative Blumeria graminis f. sp. tritici (Bgt) isolates collected from different regions of the USA. An F2 population and F2:3 lines derived from the cross PI 628024 × CItr 11349 were used in this study, and genetic analysis indicated that a single dominant gene, designated Pm63, conferred resistance to Bgt isolate OKS(14)-B-3-1. Linkage analysis located Pm63 to an interval of about 13.1 Mb on the long arm of chromosome 2B, spanning ...
Source: TAG. Theoretical and Applied Genetics - December 12, 2018 Category: Genetics & Stem Cells Authors: Tan C, Li G, Cowger C, Carver BF, Xu X Tags: Theor Appl Genet Source Type: research

Genotyping-by-sequencing based genetic mapping reveals large number of epistatic interactions for stem rot resistance in groundnut.
Abstract KEY MESSAGE: Genetic mapping identified large number of epistatic interactions indicating the complex genetic architecture for stem rot disease resistance. Groundnut (Arachis hypogaea) is an important global crop commodity and serves as a major source of cooking oil, diverse confectionery preparations and livestock feed. Stem rot disease caused by Sclerotium rolfsii is the most devastating disease of groundnut and can cause up to 100% yield loss. Genomic-assisted breeding (GAB) has potential for accelerated development of stem rot resistance varieties in short period with more precision. In this context, ...
Source: TAG. Theoretical and Applied Genetics - December 11, 2018 Category: Genetics & Stem Cells Authors: Dodia SM, Joshi B, Gangurde SS, Thirumalaisamy PP, Mishra GP, Narandrakumar D, Soni P, Rathnakumar AL, Dobaria JR, Sangh C, Chitikineni A, Chanda SV, Pandey MK, Varshney RK, Thankappan R Tags: Theor Appl Genet Source Type: research

Genetic analysis of cob resistance to F. verticillioides: another step towards the protection of maize from ear rot.
Abstract KEY MESSAGE: We lay the foundation for further research on maize resistance to Fusarium verticillioides cob rot by identifying a candidate resistance gene. Fusarium verticillioides ear rot is the most common type of maize ear rot in the Huanghuaihai Plain of China. Ear rot resistance includes cob and kernel resistance. Most of the current literature concentrates on kernel resistance, and genetic studies on cob resistance are scarce. We aimed on identifying the QTLs responsible for F. verticillioides cob rot (FCR) resistance. Twenty-eight genes associated with 48 single nucleotide polymorphisms (SNPs) were...
Source: TAG. Theoretical and Applied Genetics - December 10, 2018 Category: Genetics & Stem Cells Authors: Mu C, Gao J, Zhou Z, Wang Z, Sun X, Zhang X, Dong H, Han Y, Li X, Wu Y, Song Y, Ma P, Dong C, Chen J, Wu J Tags: Theor Appl Genet Source Type: research

Introgression reshapes recombination distribution in grapevine interspecific hybrids.
Abstract KEY MESSAGE: In grapevine interspecific hybrids, meiotic recombination is suppressed in homeologous regions and enhanced in homologous regions of recombined chromosomes, whereas crossover rate remains unchanged when chromosome pairs are entirely homeologous. Vitis rotundifolia, an American species related to the cultivated European grapevine Vitis vinifera, has a high level of resistance to several grapevine major diseases and is consequently a valuable resource for grape breeding. However, crosses between both species most often lead to very few poorly fertile hybrids. In this context, identifying geneti...
Source: TAG. Theoretical and Applied Genetics - December 8, 2018 Category: Genetics & Stem Cells Authors: Delame M, Prado E, Blanc S, Robert-Siegwald G, Schneider C, Mestre P, Rustenholz C, Merdinoglu D Tags: Theor Appl Genet Source Type: research

Divergence between bread wheat and Triticum militinae in the powdery mildew resistance QPm.tut-4A locus and its implications for cloning of the resistance gene.
J, Vrána J, Doležel J, Järve K, Valárik M Abstract A segment of Triticum militinae chromosome 7G harbors a gene(s) conferring powdery mildew resistance which is effective at both the seedling and the adult plant stages when transferred into bread wheat (T. aestivum). The introgressed segment replaces a piece of wheat chromosome arm 4AL. An analysis of segregating materials generated to positionally clone the gene highlighted that in a plant heterozygous for the introgression segment, only limited recombination occurs between the introgressed region and bread wheat 4A. Nevertheless, 75 genetic...
Source: TAG. Theoretical and Applied Genetics - December 7, 2018 Category: Genetics & Stem Cells Authors: Janáková E, Jakobson I, Peusha H, Abrouk M, Škopová M, Šimková H, Šafář J, Vrána J, Doležel J, Järve K, Valárik M Tags: Theor Appl Genet Source Type: research

Mapping resistance to Phytophthora root rot identifies independent loci from cultivated (Cicer arietinum L.) and wild (Cicer echinospermum P.H. Davis) chickpea.
Abstract KEY MESSAGE: Major QTL for Phytophthora root rot resistance have been identified in three mapping populations with independent sources of resistance contributed by C. echinospermum and C. arietinum. Phytophthora root rot (PRR) caused by the oomycete Phytophthora medicaginis is a major soil-borne disease of chickpea in Australia. With no economic in-crop control of PRR, a genetic approach to improve resistance is the most practical management option. Moderate field resistance has been incorporated in the cultivated C. arietinum variety, Yorker, and a higher level of resistance has been identified in a deri...
Source: TAG. Theoretical and Applied Genetics - December 7, 2018 Category: Genetics & Stem Cells Authors: Amalraj A, Taylor J, Bithell S, Li Y, Moore K, Hobson K, Sutton T Tags: Theor Appl Genet Source Type: research

A wheat protein kinase gene TaSnRK2.9-5A associated with yield contributing traits.
Abstract KEY MESSAGE: We developed breeder-friendly high-throughput and cost-effective KASP marker for marker-assisted selection for grain yield related traits in wheat. Plant-specific protein kinase, SnRK2s, is a major family of signaling genes associated with metabolic regulations, nutrient utilization and response to external stimuli. In the present study, three copies of TaSnRK2.9 were isolated from chromosomes 5A, 5B and 5D of wheat (Triticum aestivum L.). The coding regions of TaSnRK2.9-5A, TaSnRK2.9-5B and promoter region of TaSnRK2.9-5D were investigated for sequence polymorphism. Single nucleotide po...
Source: TAG. Theoretical and Applied Genetics - December 5, 2018 Category: Genetics & Stem Cells Authors: Ur Rehman S, Wang J, Chang X, Zhang X, Mao X, Jing R Tags: Theor Appl Genet Source Type: research

Mapping versatile QTL for soybean downy mildew resistance.
Abstract KEY MESSAGE: Three versatile QTL for soybean downy mildew resistance in Japan were detected using five RIL populations and confirmed using recombinant fixed pairs or a backcrossed line. Downy mildew reduces soybean seed quality and size. It is a problem in Japan, where 90% of soybean grown is used as food. In the USA, 33 downy mildew races have been reported, but race differentiation in Japan is unclear. To identify quantitative trait loci (QTL) for downy mildew resistance effective in the Kanto and Tohoku regions, we performed QTL analysis using five populations of recombinant inbred lines (RILs) origina...
Source: TAG. Theoretical and Applied Genetics - December 4, 2018 Category: Genetics & Stem Cells Authors: Taguchi-Shiobara F, Fujii K, Sayama T, Hirata K, Kato S, Kikuchi A, Takahashi K, Iwahashi M, Ikeda C, Kosuge K, Okano K, Hayasaka M, Tsubokura Y, Ishimoto M Tags: Theor Appl Genet Source Type: research

Across-years prediction of hybrid performance in maize using genomics.
This study on hybrid prediction in grain maize illustrated that including historical phenotypic data for training, although consisting of less related genotypes, can improve genomic prediction and enables optimization of hybrid variety development. PMID: 30498894 [PubMed - as supplied by publisher] (Source: TAG. Theoretical and Applied Genetics)
Source: TAG. Theoretical and Applied Genetics - November 29, 2018 Category: Genetics & Stem Cells Authors: Schrag TA, Schipprack W, Melchinger AE Tags: Theor Appl Genet Source Type: research

Hybrid durum wheat: heterosis of grain yield and quality traits and genetic architecture of anther extrusion.
In this study, we investigated the heterosis for grain yield and important quality traits in durum wheat of 33 hybrids built up from 24 parental lines, as well as the variation in anther extrusion and its genetic architecture in a vast collection of Central European elite durum lines. Average mid-parent heterosis for grain yield was 5.8%, and the best hybrids had a more than one ton per hectare higher grain yield than the best line cultivars. Furthermore, hybrids had a higher grain yield than lines at a given level of protein content or sedimentation value, underpinning their potential for a sustainable agriculture. Howeve...
Source: TAG. Theoretical and Applied Genetics - November 29, 2018 Category: Genetics & Stem Cells Authors: Akel W, Rapp M, Thorwarth P, Würschum T, Longin CFH Tags: Theor Appl Genet Source Type: research

Reciprocal recurrent genomic selection: an attractive tool to leverage hybrid wheat breeding.
Abstract KEY MESSAGE: Using a two-part breeding strategy based on a population improvement and a product development component can leverage hybrid wheat breeding. Despite the technological advance of methods to facilitate hybrid breeding in self-pollinating crops, line breeding is still the dominating breeding strategy. This is likely due to a higher long-term selection gain in line compared to hybrid breeding. In this respect, recent studies on two-part strategies splitting the breeding program into a population improvement and a product development component could mark a trend reversal. Here, an overview of expe...
Source: TAG. Theoretical and Applied Genetics - November 28, 2018 Category: Genetics & Stem Cells Authors: Rembe M, Zhao Y, Jiang Y, Reif JC Tags: Theor Appl Genet Source Type: research

Manipulation of crossover frequency and distribution for plant breeding.
Abstract The crossovers (COs) that occur during meiotic recombination lead to genetic diversity upon which natural and artificial selection can act. The potential of tinkering with the mechanisms of meiotic recombination to increase the amount of genetic diversity accessible for breeders has been under the research spotlight for years. A wide variety of approaches have been proposed to increase CO frequency, alter CO distribution and induce COs between non-homologous chromosomal regions. For most of these approaches, translational biology will be crucial for demonstrating how these strategies can be of practical u...
Source: TAG. Theoretical and Applied Genetics - November 27, 2018 Category: Genetics & Stem Cells Authors: Blary A, Jenczewski E Tags: Theor Appl Genet Source Type: research

Development and use of chromosome segment substitution lines as a genetic resource for crop improvement.
Abstract KEY MESSAGE: CSSLs are a complete library of introgression lines with chromosomal segments of usually a distant genotype in an adapted background and are valuable genetic resources for basic and applied research on improvement of complex traits. Chromosome segment substitution lines (CSSLs) are genetic stocks representing the complete genome of any genotype in the background of a cultivar as overlapping segments. Ideally, each CSSL has a single chromosome segment from the donor with a maximum recurrent parent genome recovered in the background. CSSL development program requires population-wide backcross b...
Source: TAG. Theoretical and Applied Genetics - November 27, 2018 Category: Genetics & Stem Cells Authors: Balakrishnan D, Surapaneni M, Mesapogu S, Neelamraju S Tags: Theor Appl Genet Source Type: research

Fine mapping and molecular marker development of the Sm gene conferring resistance to gray leaf spot (Stemphylium spp.) in tomato.
This study aimed to map and identify molecular marker tightly linked to the Sm gene for the use of marker-assisted selection in breeding. Using an F2 population derived from a cross between the resistant line '9706' and the susceptible line 'Heinz 1706', the Sm gene was mapped to a 185-kb interval between two markers, InDel343 and InDel-FT-32 on chromosome 11, which was consistent with the result of a genome-wide association study using 289 diverse accessions. An ORF predicted in this region was proved to be involved in Sm-mediated resistance through transient gene silencing and seems to be a good candidate of the Sm locus...
Source: TAG. Theoretical and Applied Genetics - November 26, 2018 Category: Genetics & Stem Cells Authors: Su X, Zhu G, Huang Z, Wang X, Guo Y, Li B, Du Y, Yang W, Gao J Tags: Theor Appl Genet Source Type: research

QTL mapping of insect resistance components of Solanum galapagense.
Abstract KEY MESSAGE: QTLs for insect resistance parameters, trichome type IV development, and more than 200 non-volatile metabolites, including 76 acyl sugars, all co-locate at the end of Chromosome 2 of Solanum galapagense. Host plant resistance is gaining importance as more and more insecticides are being banned due to environmental concerns. In tomato, resistance towards insects is found in wild relatives and has been attributed to the presence of glandular trichomes and their specific phytochemical composition. In this paper, we describe the results from a large-scale QTL mapping of data from whitefly resista...
Source: TAG. Theoretical and Applied Genetics - November 23, 2018 Category: Genetics & Stem Cells Authors: Vosman B, Kashaninia A, Van't Westende W, Meijer-Dekens F, van Eekelen H, Visser RGF, de Vos RCH, Voorrips RE Tags: Theor Appl Genet Source Type: research

Independent activation of the BoMYB2 gene leading to purple traits in Brassica oleracea.
In this study, the causal genes for the purple traits in kale, kohlrabi and cabbage were cloned using map-based cloning approach. The purple traits in all three varieties were mapped to the same locus as the BoMYB2 gene in cauliflower. Surprisingly, the insertion of Harbinger transposon of BoMYB2 in cauliflower was not found in purple kale, kohlrabi and cabbage. Sequencing of the BoMYB2 gene in purple kale and purple kohlrabi discovered a 7606 bp CACTA-like transposon in its promoter region. Transient assay and promoter activity study showed that the insertion upregulated the expression of the BoMYB2 gene. On the othe...
Source: TAG. Theoretical and Applied Genetics - November 22, 2018 Category: Genetics & Stem Cells Authors: Yan C, An G, Zhu T, Zhang W, Zhang L, Peng L, Chen J, Kuang H Tags: Theor Appl Genet Source Type: research

Fine mapping of qGL5H, a major grain length locus in barley (Hordeum vulgare L.).
Abstract KEY MESSAGE: A major grain length QTL on chromosome 5H was fine mapped from 180.5 to 1.7 Mb. Quantitative trait loci (QTLs) mapping has been used extensively in barley to detect QTLs that underlie complex traits such as grain size. In the present study, we utilised 312 double haploid lines derived from a cross between two Australian malting varieties, Vlamingh and Buloke, to dissect the genetic control of a number of grain size characteristics. Digital image analysis was used to measure grain size characteristics including length, width, thickness and plumpness which are important traits influencing ...
Source: TAG. Theoretical and Applied Genetics - November 21, 2018 Category: Genetics & Stem Cells Authors: Watt C, Zhou G, McFawn LA, Chalmers KJ, Li C Tags: Theor Appl Genet Source Type: research

Construction of introgression lines of Oryza rufipogon and evaluation of important agronomic traits.
Abstract Cultivated rice (Oryza sativa) originated from common wild rice (Oryza rufipogon) and inherited its advantages. However, during the rice domestication process, some valuable features of wild rice, such as tolerance to biotic and abiotic stress, were lost. To fully utilize wild rice germplasm resources, we constructed a set of introgression lines (ILs) using a common wild rice material from Lingshui, China. A set of high-resolution InDel molecular markers with an average interval of 2.39 Mb were designed to carry out marker-assisted selection and identification of segment characteristics. The ILs cont...
Source: TAG. Theoretical and Applied Genetics - November 21, 2018 Category: Genetics & Stem Cells Authors: Qin G, Nguyen HM, Luu SN, Wang Y, Zhang Z Tags: Theor Appl Genet Source Type: research

Loci and candidate genes in soybean that confer resistance to Fusarium graminearum.
The objective of the present study was to identify the genome-wide genetic architecture of resistance to F. graminearum in landraces and cultivated soybeans based on a growth room evaluation. The resistance levels of 314 diverse accessions were tested, and 22,888 single nucleotide polymorphisms (SNPs) with a minor allele frequency of > 0.05 were developed using the specific-locus amplified fragment sequencing (SLAF-seq) approach. Twelve SNPs were identified as associated with F. graminearum resistance, and these SNPs were located at 12 genomic regions on eight chromosomes (Chr.) and could explain 5.53-14.7...
Source: TAG. Theoretical and Applied Genetics - November 19, 2018 Category: Genetics & Stem Cells Authors: Zhang C, Zhao X, Qu Y, Teng W, Qiu L, Zheng H, Wang Z, Han Y, Li W Tags: Theor Appl Genet Source Type: research

Dissecting the genetics underlying the relationship between protein content and grain yield in a large hybrid wheat population.
In this study, we used a large population of 1604 hybrids and their 135 parental components to investigate the genetics and metabolomics underlying the negative relationship of grain yield and quality, and evaluated approaches for their joint improvement. We identified a total of nine trait-associated metabolites and show that prediction using genomic data alone resulted in the highest prediction ability for all traits. We dissected the genetic architecture of grain yield and quality-determining traits and show results of the first mapping of the derived trait grain protein deviation. Further, we provide a genetic analysis...
Source: TAG. Theoretical and Applied Genetics - November 19, 2018 Category: Genetics & Stem Cells Authors: Thorwarth P, Liu G, Ebmeyer E, Schacht J, Schachschneider R, Kazman E, Reif JC, Würschum T, Longin CFH Tags: Theor Appl Genet Source Type: research

Connecting genome structural variation with complex traits in crop plants.
We describe how genome analysis methods are enabling discovery of trait-associated structural variants and their potential impact on breeding. As our understanding of complex crop genomes continues to grow, there is growing evidence that structural genome variation plays a major role in determining traits important for breeding and agriculture. Identifying the extent and impact of structural variants in crop genomes is becoming increasingly feasible with ongoing advances in the sophistication of genome sequencing technologies, particularly as it becomes easier to generate accurate long sequence reads on a genome-wide scale...
Source: TAG. Theoretical and Applied Genetics - November 17, 2018 Category: Genetics & Stem Cells Authors: Gabur I, Chawla HS, Snowdon RJ, Parkin IAP Tags: Theor Appl Genet Source Type: research

Prospects of pan-genomics in barley.
Abstract The concept of a pan-genome refers to intraspecific diversity in genome content and structure, encompassing both genes and intergenic space. Pan-genomic studies employ a combination of de novo sequence assembly and reference-based alignment to discover and genotype structural variants. The large size and complex structure of Triticeae genomes were for a long time an obstacle for genomic research in barley and its relatives. Now that a reference genome is available, computational pipelines for high-quality sequence assembly are in place, and sequence costs continue to drop, investigations into the structur...
Source: TAG. Theoretical and Applied Genetics - November 16, 2018 Category: Genetics & Stem Cells Authors: Monat C, Schreiber M, Stein N, Mascher M Tags: Theor Appl Genet Source Type: research

An evolutionarily conserved non-synonymous SNP in a leucine-rich repeat domain determines anthracnose resistance in watermelon.
This study provides a step forward in understanding anthracnose resistance in watermelon, as well as functional and evolutionary insight into leucine-rich repeat proteins. PMID: 30446794 [PubMed - as supplied by publisher] (Source: TAG. Theoretical and Applied Genetics)
Source: TAG. Theoretical and Applied Genetics - November 16, 2018 Category: Genetics & Stem Cells Authors: Jang YJ, Seo M, Hersh CP, Rhee SJ, Kim Y, Lee GP Tags: Theor Appl Genet Source Type: research

Genetic architecture of wheat stripe rust resistance revealed by combining QTL mapping using SNP-based genetic maps and bulked segregant analysis.
Abstract KEY MESSAGE: A major stripe rust resistance QTL was mapped to a 0.4 centimorgan (cM) genetic region on the long arm of chromosome 7B, using combined genome-wide linkage mapping and bulk segregant analysis. The German winter wheat cv. Centrum has displayed high levels of adult plant stripe rust resistance (APR) in field environments for many years. Here, we used the combined genome-wide linkage mapping and pool-extreme genotyping to characterize the APR resistance. One hundred and fifty-one F2:7 recombinant inbred lines derived from a cross between susceptible landrace Mingxian 169 and Centrum were evaluat...
Source: TAG. Theoretical and Applied Genetics - November 16, 2018 Category: Genetics & Stem Cells Authors: Mu J, Huang S, Liu S, Zeng Q, Dai M, Wang Q, Wu J, Yu S, Kang Z, Han D Tags: Theor Appl Genet Source Type: research

Different loci associated with root and foliar resistance to sudden death syndrome (Fusarium virguliforme) in soybean.
The objectives of this study were to (1) map the loci associated with root and foliar resistance to F. virguliforme infection and (2) decipher the relationships between root infection, foliar damage, and plot yield. A mapping population consisting of 153 F4-derived recombinant inbred lines from the cross U01-390489 × E07080 was genotyped by SoySNP6 K BeadChip assay. Both foliar damage and F. virguliforme colonization in roots were investigated in the field, and a weak positive correlation was identified between them. Foliar damage had a stronger negative correlation with plot yield than F. virgulif...
Source: TAG. Theoretical and Applied Genetics - November 16, 2018 Category: Genetics & Stem Cells Authors: Tan R, Collins PJ, Wang J, Wen Z, Boyse JF, Laurenz RG, Gu C, Jacobs JL, Song Q, Chilvers MI, Wang D Tags: Theor Appl Genet Source Type: research

Molecular characterization of genomic regions for resistance to Pythium ultimum var. ultimum in the soybean cultivar Magellan.
The objective of this research was to identify quantitative trait loci (QTL) for resistance to P. ultimum var. ultimum in a recombinant inbred line population derived from a cross of 'Magellan' (moderately resistant) and PI 438489B (susceptible). Two different mapping approaches were utilized: the universal soybean linkage panel (USLP 1.0) and the bin map constructed from whole genome re-sequencing (WGRS) technology. Two genomic regions associated with variation in three disease-related parameters were detected using both approaches, with the bin map providing higher resolution. Using WGRS, the first QTL were mapped within...
Source: TAG. Theoretical and Applied Genetics - November 15, 2018 Category: Genetics & Stem Cells Authors: Klepadlo M, Balk CS, Vuong TD, Dorrance AE, Nguyen HT Tags: Theor Appl Genet Source Type: research

A major QTL and candidate genes for capsaicinoid biosynthesis in the pericarp of Capsicum chinense revealed using QTL-seq and RNA-seq.
Abstract KEY MESSAGE: A major QTL and candidate genes controlling capsaicinoid content in the pericarp were identified by QTL-seq and RNA-seq in Capsicum chinense. Capsaicinoid biosynthesis was previously thought to be restricted to the placental tissue; however, the recent discovery of their biosynthesis in the pericarp provides new opportunities to increase the capsaicinoid content in pepper fruits. Currently, the genetic mechanisms regulating capsaicinoid biosynthesis in the pericarp remain unknown. Here, we performed quantitative trait loci (QTL) mapping and RNA sequencing (RNA-seq) to reveal the genes control...
Source: TAG. Theoretical and Applied Genetics - November 13, 2018 Category: Genetics & Stem Cells Authors: Park M, Lee JH, Han K, Jang S, Han J, Lim JH, Jung JW, Kang BC Tags: Theor Appl Genet Source Type: research

Enhancing grain size in durum wheat using RNAi to knockdown GW2 genes.
Abstract KEY MESSAGE: Knocking down GW2 enhances grain size by regulating genes encoding the synthesis of cytokinin, gibberellin, starch and cell wall. Raising crop yield is a priority task in the light of the continuing growth of the world's population and the inexorable loss of arable land to urbanization. Here, the RNAi approach was taken to reduce the abundance of Grain Weight 2 (GW2) transcript in the durum wheat cultivar Svevo. The effect of the knockdown was to increase the grains' starch content by 10-40%, their width by 4-13% and their surface area by 3-5%. Transcriptomic profiling, based on a quantitativ...
Source: TAG. Theoretical and Applied Genetics - November 13, 2018 Category: Genetics & Stem Cells Authors: Sestili F, Pagliarello R, Zega A, Saletti R, Pucci A, Botticella E, Masci S, Tundo S, Moscetti I, Foti S, Lafiandra D Tags: Theor Appl Genet Source Type: research

Identification of a major QTL on chromosome arm 2AL for reducing yellow rust severity from a Chinese wheat landrace with evidence for durable resistance.
Abstract KEY MESSAGE: A QTL on 2AL for reducing yellow rust severity was identified from a Chinese wheat landrace, being more effective than Yr18, with evidence for durable resistance from field observations. Utilization of wheat resistance is an important strategy to control yellow rust. The Chinese wheat landrace Hong Qimai (HQM) and the advanced breeding line AQ24788-83 (AQ; a progeny of HQM) can significantly reduce disease severity at the adult-plant growth stage. HQM has maintained adult-plant resistance for a prolonged period of time. To study the inheritance of the resistance, 126 recombinant inbred lines ...
Source: TAG. Theoretical and Applied Genetics - November 13, 2018 Category: Genetics & Stem Cells Authors: Wang Z, Ren J, Du Z, Che M, Zhang Y, Quan W, Jiang X, Ma Y, Zhao Y, Zhang Z Tags: Theor Appl Genet Source Type: research

Organelle DNA contents and starch accumulation in potato tubers.
Abstract KEY MESSAGE: Starch contents were found to be positively correlated with organelle/nuclear DNA ratios, suggesting that these ratios are involved in starch accumulation and may serve as a target trait in genetic engineering and a biomarker in breeding for improving the dry matter and starch production in potato. Starch is the main dry matter component of various staple food crops, including potato. Starch synthesis and accumulation is in plastids, uses sugar, consumes cellular energy, and requires active expression of starch synthesis genes. We hypothesized that the plastid/nuclear DNA ratios and mitochond...
Source: TAG. Theoretical and Applied Genetics - November 3, 2018 Category: Genetics & Stem Cells Authors: Niu S, Zhang G, Li X, Haroon M, Si H, Fan G, Li XQ Tags: Theor Appl Genet Source Type: research

Genetic and transcriptional variations in NRAMP-2 and OPAQUE1 genes are associated with salt stress response in wheat.
This study identified genetic and molecular components of salt stress response that are associated with Na+-uptake, shoot Na+/K+ ratio, ABS/RC, DIo/RC, and grain quality traits and upon functional validation would facilitate the development of gene-specific markers that could be deployed to improve salinity tolerance in wheat. PMID: 30392081 [PubMed - as supplied by publisher] (Source: TAG. Theoretical and Applied Genetics)
Source: TAG. Theoretical and Applied Genetics - November 3, 2018 Category: Genetics & Stem Cells Authors: Oyiga BC, Ogbonnaya FC, Sharma RC, Baum M, Léon J, Ballvora A Tags: Theor Appl Genet Source Type: research

Small ad hoc versus large general training populations for genomewide selection in maize biparental crosses.
Abstract KEY MESSAGE: For genomewide selection in each biparental population, it is better to use a smaller ad hoc training population than a single, large training population. In genomewide selection, different types of training populations can be used for a biparental population made from homozygous parents (A and B). Our objective was to determine whether the response to selection (R) and predictive ability (rMP) in an A/B population are higher with a large training population that is used for all biparental crosses, or with a smaller ad hoc training population highly related to the A/B population. We studied 9...
Source: TAG. Theoretical and Applied Genetics - November 2, 2018 Category: Genetics & Stem Cells Authors: Brandariz SP, Bernardo R Tags: Theor Appl Genet Source Type: research

Pid3-I1 is a race-specific partial-resistance allele at the Pid3 blast resistance locus in rice.
Abstract KEY MESSAGE: The rice blast resistance QTL detected on chromosome 6 in MC276 is Pid3-I1, one of the multiple alleles at the Pid3 locus. Pid3-I1 shows race-specific partial resistance. Many of the quantitative trait loci (QTLs) for rice blast resistance reported to date remain unidentified. In the present study, we focused on qBRM6.2, a known blast-resistance QTL in experimental resistant rice line MC276. A CO39 near-isogenic line (NIL) carrying qBRM6.2 from MC276 was developed here, and we showed that qBRM6.2 resistance was partial but race specific to Japanese blast isolates using the NIL. Because defens...
Source: TAG. Theoretical and Applied Genetics - November 2, 2018 Category: Genetics & Stem Cells Authors: Inukai T, Nagashima S, Kato M Tags: Theor Appl Genet Source Type: research

Correction to: Pm223899, a new recessive powdery mildew resistance gene identified in Afghanistan landrace PI 223899.
Abstract Unfortunately, the caption of Fig. 2 was incorrectly published in the original publication. The complete correct caption should read as follows. PMID: 30386915 [PubMed - as supplied by publisher] (Source: TAG. Theoretical and Applied Genetics)
Source: TAG. Theoretical and Applied Genetics - November 1, 2018 Category: Genetics & Stem Cells Authors: Li G, Carver BF, Cowger C, Bai G, Xu X Tags: Theor Appl Genet Source Type: research

Identification and mapping of two independent recessive loci for the root hairless mutant phenotype in soybean.
In conclusion, we partially uncovered the genetic mechanism underlying root hair formation in soybean. Namely, two independent recessive loci, qRHLa and qRHLb, containing several candidate genes were predicted to control the root hairless mutant RBC-HL. PMID: 30382310 [PubMed - as supplied by publisher] (Source: TAG. Theoretical and Applied Genetics)
Source: TAG. Theoretical and Applied Genetics - October 31, 2018 Category: Genetics & Stem Cells Authors: Yang Y, Lv H, Liao H Tags: Theor Appl Genet Source Type: research

Modeling copy number variation in the genomic prediction of maize hybrids.
eto R Abstract KEY MESSAGE: Our study indicates that copy variants may play an essential role in the phenotypic variation of complex traits in maize hybrids. Moreover, predicting hybrid phenotypes by combining additive-dominance effects with copy variants has the potential to be a viable predictive model. Non-additive effects resulting from the actions of multiple loci may influence trait variation in single-cross hybrids. In addition, complementation of allelic variation could be a valuable contributor to hybrid genetic variation, especially when crossing inbred lines with higher contents of copy gains. With this...
Source: TAG. Theoretical and Applied Genetics - October 31, 2018 Category: Genetics & Stem Cells Authors: Lyra DH, Galli G, Alves FC, Granato ÍSC, Vidotti MS, Bandeira E Sousa M, Morosini JS, Crossa J, Fritsche-Neto R Tags: Theor Appl Genet Source Type: research

Lessons from natural variations: artificially induced heading date variations for improvement of regional adaptation in rice.
Abstract KEY MESSAGE: New strategy of breeding by modulating key heading date gene Ehd1 to enhance the variations of heading date regardless of genetic background for better adaptation to local environment in rice. Flowering time (or heading date) is an important quantitative trait in rice (Oryza sativa) that determines its adaptation to specific cultivation areas and growing seasons. However, breeding of flowering time is currently relying on laborious selections and combinations of different alleles of various genes. Here, we cloned a cis-variant allele of Ehd1 that regulated not only heading date but also yield...
Source: TAG. Theoretical and Applied Genetics - October 31, 2018 Category: Genetics & Stem Cells Authors: Hu Y, Li S, Xing Y Tags: Theor Appl Genet Source Type: research

Mapping of the male sterile mutant gene ftms in Brassica rapa L. ssp. pekinensis via BSR-Seq combined with whole-genome resequencing.
In this study, we derived a male sterile mutant (ftms) from Chinese cabbage DH line 'FT' by irradiating microspores with 60Co γ-rays and realized the rapid trait transformation from male fertility to sterility for creating valuable breeding materials. Genetic analysis indicated that the male sterile trait is controlled by a single recessive nuclear gene, ftms. Microspore development in mutant ftms was aborted at the tetrad stage and associated with severely retarded degeneration and vacuolation of tapetum. Using BSR-seq analysis, the candidate region for ftms was mapped on chromosome A05. A large F2 population was cr...
Source: TAG. Theoretical and Applied Genetics - October 31, 2018 Category: Genetics & Stem Cells Authors: Tan C, Liu Z, Huang S, Feng H Tags: Theor Appl Genet Source Type: research

Targeted recombination to increase genetic gain in self-pollinated species.
Abstract KEY MESSAGE: If we can induce or select for recombination at targeted marker intervals, genetic gains for quantitative traits in self-pollinated species may be doubled. Targeted recombination refers to inducing or selecting for a recombination event at genomic positions that maximize genetic gain in a cross. A previous study indicated that targeted recombination could double the rate of genetic gains in maize (Zea mays L.), a cross-pollinated crop for which historical genetic gains have been large. Our objectives were to determine whether targeted recombination can sufficiently increase predicted gains in...
Source: TAG. Theoretical and Applied Genetics - October 30, 2018 Category: Genetics & Stem Cells Authors: Ru S, Bernardo R Tags: Theor Appl Genet Source Type: research

Transfer of stem rust resistance gene SrB from Thinopyrum ponticum into wheat and development of a closely linked PCR-based marker.
We report transfer of a rust resistance gene named SrB, on the 6Ae#3 chromosome, to wheat by recombination with the 6Ae#1 segment carrying Sr26 and development of a linked marker. A stem rust resistance gene from a South African wheat W3757, temporarily named SrB, has been transferred onto chromosome 6A. Line W3757 is a 6Ae#3 (6D) substitution line in which the Thinopyrum ponticum chromosomes carry SrB. Crosses were made between W3757 and a T6AS·6AL-6Ae#1 recombinant line named WA-5 carrying the stem rust resistance gene Sr26 on a chromosome segment from another accession of Th. ponticum. The 6Ae#1 and 6Ae#3 chromos...
Source: TAG. Theoretical and Applied Genetics - October 30, 2018 Category: Genetics & Stem Cells Authors: Mago R, Zhang P, Xia X, Zhang J, Hoxha S, Lagudah E, Graner A, Dundas I Tags: Theor Appl Genet Source Type: research

Crop resistant starch and genetic improvement: a review of recent advances.
Abstract Resistant starch (RS), as a healthy dietary fiber, meets with great human favor along with the rapid development and improvement of global living standards. RS shows direct effects in reducing postprandial blood glucose levels, serum cholesterol levels and glycemic index. Therefore, RS plays an important role in preventing and improving non-communicable diseases, such as obesity, diabetes, colon cancer, cardiovascular diseases and chronic kidney disease. In addition, RS leads to its potential applied value in the development of high-quality foodstuffs, such as bread, noodles and dumplings. This paper revi...
Source: TAG. Theoretical and Applied Genetics - October 29, 2018 Category: Genetics & Stem Cells Authors: Xia J, Zhu D, Wang R, Cui Y, Yan Y Tags: Theor Appl Genet Source Type: research

Development and molecular cytogenetic identification of a new wheat-rye 4R chromosome disomic addition line with resistances to powdery mildew, stripe rust and sharp eyespot.
Abstract KEY MESSAGE: A wheat-rye 4R chromosome disomic addition line with resistances to powdery mildew, stripe rust, sharp eyespot and high kernel number per spike was developed and characterized by molecular cytogenetic method as novel resistant germplasm. Rye (Secale cereale L.), a close relative of common wheat, is an important and valuable gene donor with multiple disease resistance for wheat improvement. However, resistance genes derived from rye have successively lost resistance to pathogens due to the coevolution of pathogen virulence and host resistance. Development and identification of new effective re...
Source: TAG. Theoretical and Applied Genetics - October 29, 2018 Category: Genetics & Stem Cells Authors: An D, Ma P, Zheng Q, Fu S, Li L, Han F, Han G, Wang J, Xu Y, Jin Y, Luo Q, Zhang X Tags: Theor Appl Genet Source Type: research

Identification of a gene responsible for cytoplasmic male-sterility in onions (Allium cepa L.) using comparative analysis of mitochondrial genome sequences of two recently diverged cytoplasms.
Abstract KEY MESSAGE: Almost identical mitochondrial genome sequences of two recently diverged male-fertile normal and male-sterile CMS-T-like cytoplasms were obtained in onions. A chimeric gene, orf725 , was found to be a CMS-inducing gene. In onions (Allium cepa L.), cytoplasmic male-sterility (CMS) has been widely used in hybrid seed production. Two types of CMS (CMS-S and CMS-T) have been reported in onions. A complete mitochondrial genome sequence of the CMS-S cytoplasm has been reported in our previous study. Draft mitochondrial genome sequences of male-fertile normal and CMS-T-like cytoplasms are reported i...
Source: TAG. Theoretical and Applied Genetics - October 29, 2018 Category: Genetics & Stem Cells Authors: Kim B, Yang TJ, Kim S Tags: Theor Appl Genet Source Type: research

Delimitation of wheat ph1b deletion and development of ph1b-specific DNA markers.
Abstract KEY MESSAGE: We detected the deletion breakpoints of wheat ph1b mutant and the actual size of the deletion. Also, we developed ph1b deletion-specific markers useful for ph1b-mediated gene introgression and genome studies. The Ph1 (pairing homoeologous) locus has been considered a major genetic system for the diploidized meiotic behavior of the allopolyploid genome in wheat. It functions as a defense system against meiotic homoeologous pairing and recombination in polyploid wheat. A large deletion of the genomic region harboring Ph1 on the long arm of chromosome 5B (5BL) led to the ph1b mutant in hexaploid...
Source: TAG. Theoretical and Applied Genetics - October 20, 2018 Category: Genetics & Stem Cells Authors: Gyawali Y, Zhang W, Chao S, Xu S, Cai X Tags: Theor Appl Genet Source Type: research

The Sorghum QTL Atlas: a powerful tool for trait dissection, comparative genomics and crop improvement.
We describe the development and application of the Sorghum QTL Atlas, a high-resolution, open-access research platform to facilitate candidate gene identification across three cereal species, sorghum, maize and rice. The mechanisms governing the genetic control of many quantitative traits are only poorly understood and have yet to be fully exploited. Over the last two decades, over a thousand QTL and GWAS studies have been published in the major cereal crops including sorghum, maize and rice. A large body of information has been generated on the genetic basis of quantitative traits, their genomic location, allelic effects ...
Source: TAG. Theoretical and Applied Genetics - October 20, 2018 Category: Genetics & Stem Cells Authors: Mace E, Innes D, Hunt C, Wang X, Tao Y, Baxter J, Hassall M, Hathorn A, Jordan D Tags: Theor Appl Genet Source Type: research

Speed breeding orphan crops.
Abstract KEY MESSAGE: This review explores how speed breeding protocols that hasten plant growth and development could be applied to shorten breeding cycles and accelerate research activities in orphan crops. There is a growing need for the agri-food sector to sustainably produce larger quantities of higher-quality food, feed and fuel using fewer resources, within the context of changing agroclimatic conditions. Meeting this challenge will require the accelerated development and dissemination of improved plant varieties and substantial improvement of agricultural practices. Speed breeding protocols that shorten pl...
Source: TAG. Theoretical and Applied Genetics - October 19, 2018 Category: Genetics & Stem Cells Authors: Chiurugwi T, Kemp S, Powell W, Hickey LT Tags: Theor Appl Genet Source Type: research

Construction of a high-density linkage map and QTL detection of downy mildew resistance in Vitis aestivalis-derived 'Norton'.
Abstract KEY MESSAGE: A major QTL for downy mildew resistance was detected on chromosome 18 (Rpv27) in Vitis aestivalis-derived 'Norton' based on a high-resolution linkage map with SNP and SSR markers as well as 2 years of field and laboratory phenotyping data. Grapevine downy mildew caused by the oomycete Plasmopara viticola is one of the most widespread and destructive diseases, particularly in humid viticultural areas where it damages green tissues and defoliates vines. Traditional Vitis vinifera wine grape cultivars are susceptible to downy mildew whereas several North American and a few Asian cultivars p...
Source: TAG. Theoretical and Applied Genetics - October 19, 2018 Category: Genetics & Stem Cells Authors: Sapkota S, Chen LL, Yang S, Hyma KE, Cadle-Davidson L, Hwang CF Tags: Theor Appl Genet Source Type: research